Remove lupus import test

Author: aarmey

RISE/imports.py

@@ -59,8 +59,7 @@ def import_lupus(geneThreshold: float = 0.1) -> anndata.AnnData:
     'SLE_status': SLE status: healthy or SLE}
 
     """
-    X = anndata.read_h5ad("/opt/andrew/lupus/lupus.h5ad")
-    X = anndata.AnnData(X.raw.X, X.obs, X.raw.var, X.uns, X.obsm)
+    X = anndata.read_h5ad("/opt/andrew/lupus/raw_lupus.h5ad", backed="r")
 
     protein = anndata.read_h5ad("/opt/andrew/lupus/Lupus_study_protein_adjusted.h5ad")
     protein_df = protein.to_df()

RISE/tests/test_import.py

@@ -6,14 +6,15 @@
 import pytest
 
 from ..imports import (
-    import_lupus,
     import_thomson,
 )
 
 
 @pytest.mark.parametrize(
     "import_func",
-    [import_thomson, import_lupus],
+    [
+        import_thomson,
+    ],
 )
 def test_imports(import_func):
     """Test import functions."""

pyproject.toml

@@ -22,7 +22,7 @@ dependencies = [
     "pacmap>=0.7.1",
     "tqdm>=4.66.1",
     "tlviz>=0.1.1",
-    "doubletdetection >=4.2",
+    "doubletdetection>=4.3",
     "statsmodels>=0.14.1",
     "dask[dataframe]>=2024.3.1",
     "ortools>=9.12.4544",
@@ -48,7 +48,6 @@ dev-dependencies = [
     "scanorama>=1.7.4",
     "harmonypy>=0.0.10",
     "scib>=1.1.5",
-    "scvi-tools>=1.2.1",
 ]